[r] [WIP] Add support for reading v5 assays from an axis query #3008
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Seurat v5 adds support for ragged arrays, where not every `X` layer has exactly the same cells and features. To handle this, ragged `X` layers need to be re-indexed and re-shaped on ingestion to resize down to only the data present Modified SOMA methods: - `SOMAExperimentAxisQuery$to_seurat()` and `SOMAExperimentAxisQuery$to_seurat_assay()`: now read in as v5 assays New SOMA methods: - `SOMAExperimentAxisQuery$private$.to_seurat_assay_v5()`: helper method to read in ragged and non-ragged arrays into a v5 assay; note this method only handles expression layers, all other assay-level information is handled by parent `$to_seurat_assay()` to share code with v3 assay outgestion Requires #2523 and #3007 [SC-52261](https://app.shortcut.com/tiledb-inc/story/52261/)
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johnkerl
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Nov 7, 2024
| @@ -767,7 +775,23 @@ SOMAExperimentAxisQuery <- R6::R6Class( | |||
| "'drop_levels' must be TRUE or FALSE" = isTRUE(drop_levels) || | |||
| isFALSE(drop_levels) | |||
| ) | |||
| match.arg(version, choices = "v3") | |||
| assay_hint <- names(.assay_version_hint()) | |||
| # Get the assay version | |||
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| # Get the assay version | |
| # Get the Seurat assay version |
| check_package('SeuratObject', version = '5.0.2') | ||
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| # Create dummy layer to initialize v5 assay | ||
| lname <- SeuratObject::RandomName(length = 7L) |
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| lname <- SeuratObject::RandomName(length = 7L) | |
| layer_name <- SeuratObject::RandomName(length = 7L) |
| ) | ||
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| # Read in layers | ||
| for (lyr in layers) { |
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| for (lyr in layers) { | |
| for (layer_name in layer_names) { |
| } | ||
| } | ||
| } | ||
| lcells <- cells |
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| lcells <- cells | |
| layer_cells <- cells |
| } | ||
| } | ||
| lcells <- cells | ||
| lfeatures <- features |
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| lfeatures <- features | |
| layer_features <- features |
| if (is.null(tbl)) { | ||
| next | ||
| } | ||
| sdx <- vector("list", length = length(dnames)) |
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I have no idea what sdx means. Please use a longer name that indicates what this means.
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| obsv <- seq.int(to = n_obs) | ||
| varv <- seq.int(to = n_var) | ||
| nd <- seq(from = 0L, to = 1L, by = 0.1) |
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nd = number of dimensions? Please spell out with an informative name.
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Seurat v5 adds support for ragged arrays, where not every
Xlayer has exactly the same cells and features. To handle this, raggedXlayers need to be re-indexed and re-shaped on ingestion to resize down to only the data presentModified SOMA methods:
SOMAExperimentAxisQuery$to_seurat()andSOMAExperimentAxisQuery$to_seurat_assay(): now read in as v5 assaysNew SOMA methods:
SOMAExperimentAxisQuery$private$.to_seurat_assay_v5(): helper method to read in ragged and non-ragged arrays into a v5 assay; note this method only handles expression layers, all other assay-level information is handled by parent$to_seurat_assay()to share code with v3 assay outgestionRequires #2523 and #3007
SC-52261